cooler2bedpe {HiCcompare} | R Documentation

## Read a .cool file into R and output the data in BEDPE format

### Description

Read a .cool file into R and output the data in BEDPE format

### Usage

    cooler2bedpe(path)

### Arguments

`path` | The path to a .cool file on your disk.

### Details

.cool files are HDF5 containers that store Hi-C data. Many public Hi-C datasets are available in .cool format on the mirnylab ftp site ftp://cooler.csail.mit.edu/coolers. To use these files in HiCcompare simply download the .cool file and read it into R using this function. This function will dump the contents of the file and format them into BEDPE format in R. The resulting object cant then be used in HiCcompare.

### Value

A list with two items. Item 1, "cis" contains the intra-chromosomal contact matrices, one per chromosome. Item 2, "trans" contains the inter-chromsomal contact matrix.

### Examples

    ## Not run:
     dat <- cooler2bedpe(path = "path/to/cool/file.cool")

    ## End(Not run)

[Package HiCcompare version 1.8.0 Index]